[2023-03-14 13:46:33,108] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:46:33,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:46:33,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference
[2023-03-14 13:46:34,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:46:34,184] [INFO] Task started: Prodigal
[2023-03-14 13:46:34,185] [INFO] Running command: cat /var/lib/cwl/stg43e3d47d-5b96-420a-bc99-c751e6c5a6bb/OceanDNA-b41655.fa | prodigal -d OceanDNA-b41655/cds.fna -a OceanDNA-b41655/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:46:37,157] [INFO] Task succeeded: Prodigal
[2023-03-14 13:46:37,158] [INFO] Task started: HMMsearch
[2023-03-14 13:46:37,158] [INFO] Running command: hmmsearch --tblout OceanDNA-b41655/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference/reference_markers.hmm OceanDNA-b41655/protein.faa > /dev/null
[2023-03-14 13:46:37,321] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:46:37,322] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg43e3d47d-5b96-420a-bc99-c751e6c5a6bb/OceanDNA-b41655.fa]
[2023-03-14 13:46:37,329] [INFO] Query marker FASTA was written to OceanDNA-b41655/markers.fasta
[2023-03-14 13:46:37,331] [INFO] Task started: Blastn
[2023-03-14 13:46:37,331] [INFO] Running command: blastn -query OceanDNA-b41655/markers.fasta -db /var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference/reference_markers.fasta -out OceanDNA-b41655/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:46:37,862] [INFO] Task succeeded: Blastn
[2023-03-14 13:46:37,862] [INFO] Selected 15 target genomes.
[2023-03-14 13:46:37,863] [INFO] Target genome list was writen to OceanDNA-b41655/target_genomes.txt
[2023-03-14 13:46:37,875] [INFO] Task started: fastANI
[2023-03-14 13:46:37,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e3d47d-5b96-420a-bc99-c751e6c5a6bb/OceanDNA-b41655.fa --refList OceanDNA-b41655/target_genomes.txt --output OceanDNA-b41655/fastani_result.tsv --threads 1
[2023-03-14 13:46:43,656] [INFO] Task succeeded: fastANI
[2023-03-14 13:46:43,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:46:43,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:46:43,657] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:46:43,657] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:46:43,657] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-14 13:46:43,657] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41655/tc_result.tsv
[2023-03-14 13:46:43,657] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:46:43,657] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:46:43,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference/checkm_data
[2023-03-14 13:46:43,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:46:43,662] [INFO] Task started: CheckM
[2023-03-14 13:46:43,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41655/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41655/checkm_input OceanDNA-b41655/checkm_result
[2023-03-14 13:46:57,240] [INFO] Task succeeded: CheckM
[2023-03-14 13:46:57,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.84%
Contamintation: 5.01%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:46:57,242] [INFO] ===== Completeness check finished =====
[2023-03-14 13:46:57,242] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:46:57,243] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41655/markers.fasta)
[2023-03-14 13:46:57,244] [INFO] Task started: Blastn
[2023-03-14 13:46:57,244] [INFO] Running command: blastn -query OceanDNA-b41655/markers.fasta -db /var/lib/cwl/stg9ef97443-7d6b-4b3d-b088-2737a49b51d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41655/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:46:58,027] [INFO] Task succeeded: Blastn
[2023-03-14 13:46:58,028] [INFO] Selected 7 target genomes.
[2023-03-14 13:46:58,028] [INFO] Target genome list was writen to OceanDNA-b41655/target_genomes_gtdb.txt
[2023-03-14 13:46:58,032] [INFO] Task started: fastANI
[2023-03-14 13:46:58,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e3d47d-5b96-420a-bc99-c751e6c5a6bb/OceanDNA-b41655.fa --refList OceanDNA-b41655/target_genomes_gtdb.txt --output OceanDNA-b41655/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:46:59,218] [INFO] Task succeeded: fastANI
[2023-03-14 13:46:59,223] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:46:59,223] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902605165.1	s__CACNXK01 sp902605165	96.7152	114	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	96.16	96.16	0.76	0.76	2	conclusive
GCA_902557575.1	s__CACNXK01 sp902557575	89.2231	121	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622845.1	s__CACNXK01 sp902622845	88.9903	117	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	97.97	96.57	0.95	0.93	8	-
GCA_902518715.1	s__CACNXK01 sp902518715	88.981	103	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	96.76	95.66	0.81	0.77	7	-
GCA_902594005.1	s__CACNXK01 sp902594005	88.7107	106	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541365.1	s__CACNXK01 sp902541365	88.3347	106	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	99.92	99.92	0.82	0.82	2	-
GCA_902538705.1	s__CACNXK01 sp902538705	87.1706	94	127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACNXK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:46:59,223] [INFO] GTDB search result was written to OceanDNA-b41655/result_gtdb.tsv
[2023-03-14 13:46:59,224] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:46:59,224] [INFO] DFAST_QC result json was written to OceanDNA-b41655/dqc_result.json
[2023-03-14 13:46:59,224] [INFO] DFAST_QC completed!
[2023-03-14 13:46:59,224] [INFO] Total running time: 0h0m26s